The command dumpSNP is intended for internal use only, and creates a tab delimited text file from one or more SNP containing binary files generated during assembly. SNP binary files include those with the .snpExt suffix contained in an .assembly package as well as those with either the .coverage.missingSNP or .nocoverage.missingSNP suffix contained in the _shared folder. To convert all the .snpExt files in a package simply use the .assembly name.
|Parameter||Description||Allowed values (defaults underlined)|
|file||(required) Specifies the path and name of .assembly package (all SNP files will be included), one or more individual .snpExt files or either/both of the missingSNP files.||[directory/filename enclosed in quotes]|
|output||(required) Specifies the path and name of the output file.||[directory/filename enclosed in quotes]|
|refPos_end||To export SNPs with positions lower than this value.||[number]|
|refPos_start||To export SNPs with positions higher than this value.||[number]|
|snp_maxProbNonrefToCall||Lower limit for probability scores for exported SNPs.||[number]|
|snp_minProbNonrefToCall||Lower limit for probability scores for exported SNPs.||[number]|
|snp_type||Specifies which SNP file from the .assembly to use as an input.||[simple|SNP|missing|user|stats|userIDOnly]|
|templateID||Defines the template for which the SNP will be exported.||[number]|
|onefile||Defines whether all SNPs should be placed into one file.||[true|false]|
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